From d02cef83c3c0b3f3098df1a7e7eeaf90430f784a Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Thu, 8 Feb 2024 15:54:32 +0300
Subject: R/qtl2 QC: Set up scaffolding for QC UI

Set up the scaffolding for the flows and UI that will be used when
running QC against the uploaded R/qtl2 bundle.

This will be fleshed out later, and the UI is likely to change
somewhat, down the line.
---
 scripts/qc_on_rqtl2_bundle.py | 42 ++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 42 insertions(+)
 create mode 100644 scripts/qc_on_rqtl2_bundle.py

(limited to 'scripts')

diff --git a/scripts/qc_on_rqtl2_bundle.py b/scripts/qc_on_rqtl2_bundle.py
new file mode 100644
index 0000000..5802f3a
--- /dev/null
+++ b/scripts/qc_on_rqtl2_bundle.py
@@ -0,0 +1,42 @@
+"""Run Quality Control checks on R/qtl2 bundle."""
+import sys
+from logging import getLogger, StreamHandler
+
+from redis import Redis
+
+from qc_app import jobs
+from qc_app.db_utils import database_connection
+from qc_app.check_connections import check_db, check_redis
+
+from scripts.cli_parser import init_cli_parser
+from scripts.redis_logger import setup_redis_logger
+
+def run_qc(_args):
+    """Run the QC programs."""
+    return 1
+
+if __name__ == "__main__":
+    def main():
+        """Enter R/qtl2 bundle QC runner."""
+        args = init_cli_parser(
+            "qc-on-rqtl2-bundle", "Run QC on R/qtl2 bundle.").parse_args()
+        check_redis(args.redisuri)
+        check_db(args.databaseuri)
+
+        logger = getLogger("qc-on-rqtl2-bundle")
+        logger.addHandler(StreamHandler(stream=sys.stderr))
+        logger.setLevel("DEBUG")
+
+        fqjobid = jobs.job_key(args.redisprefix, args.jobid)
+        with (database_connection(args.databaseuri) as _dbconn,
+              Redis.from_url(args.redisuri, decode_responses=True) as rconn):
+            logger.addHandler(setup_redis_logger(
+                rconn, fqjobid, f"{fqjobid}:log-messages",
+                args.redisexpiry))
+
+            exitcode = run_qc(args)
+            rconn.hset(
+                jobs.job_key(args.redisprefix, args.jobid), "exitcode", exitcode)
+            return exitcode
+
+    sys.exit(main())
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